Update template to v0.3.1 (#806)

Co-authored-by: scverse-bot <None>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Philipp A <[email protected]>

.cruft.json

@@ -1,7 +1,7 @@
 {
     "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
-    "checkout": "v0.3.0",
+    "commit": "586b1652162ff7994b0070a034023d64289ae416",
+    "checkout": "v0.3.1",
     "context": {
         "cookiecutter": {
             "project_name": "squidpy",
@@ -13,7 +13,8 @@
             "project_repo": "https://github.com/scverse/squidpy",
             "license": "BSD 3-Clause License",
             "_copy_without_render": [
-                ".github/workflows/**.yaml",
+                ".github/workflows/build.yaml",
+                ".github/workflows/test.yaml",
                 "docs/_templates/autosummary/**.rst"
             ],
             "_render_devdocs": false,

.pre-commit-config.yaml

@@ -12,11 +12,6 @@ repos:
           - id: mypy
             additional_dependencies: [numpy, pandas, types-requests]
             exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/pre-commit/mirrors-mypy/issues/33
-    - repo: https://github.com/psf/black
-      rev: 24.2.0
-      hooks:
-          - id: black
-            additional_dependencies: [toml]
     - repo: https://github.com/pre-commit/mirrors-prettier
       rev: v4.0.0-alpha.8
       hooks:
@@ -50,16 +45,14 @@ repos:
           - id: script-must-have-extension
             name: Check executable files use .sh extension
             types: [shell, executable]
-    - repo: https://github.com/asottile/blacken-docs
-      rev: 1.16.0
-      hooks:
-          - id: blacken-docs
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      # Ruff version.
       rev: v0.2.2
       hooks:
           - id: ruff
+            types_or: [python, pyi, jupyter]
             args: [--fix, --exit-non-zero-on-fix]
+          - id: ruff-format
+            types_or: [python, pyi, jupyter]
     - repo: https://github.com/pre-commit/pygrep-hooks
       rev: v1.10.0
       hooks:

.scripts/ci/download_data.py

@@ -1,4 +1,6 @@
 #!/usr/bin/env python3
+from __future__ import annotations
+
 import argparse
 from pathlib import Path
 from typing import Any

docs/_ext/typed_returns.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 import re
-from typing import Iterable, Iterator, List
+from collections.abc import Iterable, Iterator
 
 from sphinx.application import Sphinx
 from sphinx.ext.napoleon import NumpyDocstring

docs/conf.py

@@ -4,6 +4,8 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from __future__ import annotations
+
 # -- Path setup --------------------------------------------------------------
 import os
 import sys

docs/utils.py

@@ -1,10 +1,12 @@
+from __future__ import annotations
+
 import os
 import re
 from logging import info, warning
 from pathlib import Path
 from shutil import copytree, rmtree
 from tempfile import TemporaryDirectory
-from typing import Any, Dict, ForwardRef, List, Union
+from typing import Any, ForwardRef
 
 from enchant.tokenize import Filter
 from git import Repo
@@ -14,7 +16,7 @@
 
 
 def _fetch_notebooks(repo_url: str) -> None:
-    def copy_files(repo_path: Union[str, Path]) -> None:
+    def copy_files(repo_path: str | Path) -> None:
         repo_path = Path(repo_path)
 
         for dirname in ["tutorials", "auto_examples", "gen_modules"]:
@@ -30,7 +32,7 @@ def fetch_remote(repo_url: str) -> None:
 
             copy_files(repo_dir)
 
-    def fetch_local(repo_path: Union[str, Path]) -> None:
+    def fetch_local(repo_path: str | Path) -> None:
         info(f"Fetching notebooks from local path `{repo_path}`")
         repo_path = Path(repo_path)
         if not repo_path.is_dir():
@@ -75,7 +77,7 @@ def run(self) -> list[str]:
             return []
 
 
-def _get_thumbnails(root: Union[str, Path]) -> dict[str, str]:
+def _get_thumbnails(root: str | Path) -> dict[str, str]:
     res = {}
     root = Path(root)
     thumb_path = Path(__file__).parent.parent.parent / "docs" / "source"

pyproject.toml

@@ -117,65 +117,11 @@ include-package-data = true
 
 [tool.setuptools_scm]
 
-[tool.black]
-line-length = 120
-target-version = ['py39']
-include = '\.pyi?$'
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-
-)
-'''
-
-[tool.isort]
-profile = "black"
-py_version = "38"
-skip = "docs/source/conf.py,.tox,build"
-line_length = 88
-multi_line_output = 3
-include_trailing_comma = true
-use_parentheses = true
-known_stdlib = "joblib"
-known_bio = "anndata,scanpy"
-known_num = "numpy,numba,scipy,sklearn,statsmodels,pandas,xarray,dask"
-known_plot = "matplotlib,seaborn,napari"
-known_gui = "PyQt5,superqt"
-known_img = "skimage,tifffile,dask_image"
-known_graph = "networkx"
-sections = "FUTURE,STDLIB,THIRDPARTY,BIO,NUM,GUI,PLOT,IMG,GRAPH,FIRSTPARTY,LOCALFOLDER"
-no_lines_before="LOCALFOLDER"
-balanced_wrapping = true
-force_grid_wrap = 0
-length_sort = "1"
-indent = "    "
-from_first = true
-order_by_type = true
-atomic = true
-combine_star = true
-combine_as_imports = true
-honor_noqa = true
-remove_redundant_aliases = true
-only_modified = true
-group_by_package = true
-force_alphabetical_sort_within_sections = true
-lexicographical = true
-
 [tool.hatch.version]
 source = "vcs"
 
 [tool.ruff]
+line-length = 120
 exclude = [
     ".git",
     ".tox",
@@ -185,8 +131,13 @@ exclude = [
     "dist",
     "setup.py"
 ]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
+    # line too long -> we accept long comment lines; formatter gets rid of long code lines
     "E501",
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",
@@ -243,7 +194,6 @@ ignore = [
     # "E111",
     # "E114",
 ]
-line-length = 120
 select = [
     "I", # isort
     "E", # pycodestyle
@@ -255,19 +205,22 @@ select = [
     "B", # flake8-bugbear
     "BLE", # flake8-blind-except
 ]
-unfixable = ["B", "UP", "C4", "BLE"]
-target-version = "py38"
-[tool.ruff.per-file-ignores]
-    "*/__init__.py" = ["D104", "F401"]
-    "tests/*"= ["D"]
-    "docs/*"= ["D","B"]
-    "squidpy/pl/_ligrec.py"= ["D","B"]
-    "squidpy/_constants/_pkg_constants.py"= ["D101","D102","D106"]
-    "squidpy/_constants/_constants.py"= ["D101"]
-    "squidpy/pl/_interactive/_widgets.py"= ["D"]
-    ".scripts/ci/download_data.py"= ["D","B"]
-    # "squidpy/*.py"= ["RST303"]
+unfixable = ["B", "C4", "BLE"]
+
+[tool.ruff.lint.isort]
+required-imports = ["from __future__ import annotations"]
+
+[tool.ruff.lint.per-file-ignores]
+"*/__init__.py" = ["D104", "F401"]
+"tests/*"= ["D"]
+"docs/*"= ["D","B"]
+"squidpy/pl/_ligrec.py"= ["D","B"]
+"squidpy/_constants/_pkg_constants.py"= ["D101","D102","D106"]
+"squidpy/_constants/_constants.py"= ["D101"]
+"squidpy/pl/_interactive/_widgets.py"= ["D"]
+".scripts/ci/download_data.py"= ["D","B"]
+# "squidpy/*.py"= ["RST303"]
 
-[tool.ruff.flake8-tidy-imports]
+[tool.ruff.lint.flake8-tidy-imports]
 # Disallow all relative imports.
 ban-relative-imports = "all"

src/squidpy/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from importlib import metadata
 
 from squidpy import datasets, gr, im, pl, read, tl

src/squidpy/_constants/_constants.py

@@ -1,5 +1,7 @@
 """Constants that user deals with."""
 
+from __future__ import annotations
+
 from enum import unique
 
 from squidpy._constants._utils import ModeEnum

src/squidpy/_constants/_pkg_constants.py

@@ -2,7 +2,8 @@
 
 from __future__ import annotations
 
-from typing import Any, Callable, Mapping, Optional, Sequence, Union
+from collections.abc import Callable, Mapping, Sequence
+from typing import Any
 
 from anndata import AnnData
 

src/squidpy/_constants/_utils.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 
 from abc import ABC, ABCMeta
+from collections.abc import Mapping
 from enum import Enum, EnumMeta
 from functools import wraps
-from typing import Any, Callable, Mapping, Tuple
+from typing import Any, Callable
 
 
 def _pretty_raise_enum(cls: type[ModeEnum], fun: Callable[..., Any]) -> Callable[..., Any]:
@@ -33,7 +34,9 @@ class ErrorFormatterABC(ABC):
     @classmethod
     def _format(cls, value: Enum) -> str:
         return cls.__error_format__.format(
-            value, cls.__name__, [m.value for m in cls.__members__.values()]  # type: ignore[attr-defined]
+            value,
+            cls.__name__,
+            [m.value for m in cls.__members__.values()],  # type: ignore[attr-defined]
         )
 
 

src/squidpy/_utils.py

@@ -5,21 +5,13 @@
 import functools
 import inspect
 import warnings
+from collections.abc import Generator, Hashable, Iterable, Sequence
 from contextlib import contextmanager
 from enum import Enum
 from multiprocessing import Manager, cpu_count
 from queue import Queue
 from threading import Thread
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Callable,
-    Generator,
-    Hashable,
-    Iterable,
-    Sequence,
-    Union,  # noqa: F401
-)
+from typing import TYPE_CHECKING, Any, Callable
 
 import joblib as jl
 import numpy as np

src/squidpy/datasets/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from squidpy.datasets._10x_datasets import visium
 from squidpy.datasets._dataset import *  # noqa: F403
 from squidpy.datasets._image import *  # noqa: F403

src/squidpy/datasets/_dataset.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from copy import copy
 
 from squidpy.datasets._utils import AMetadata

src/squidpy/datasets/_image.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from copy import copy
 
 from squidpy.datasets._utils import ImgMetadata

src/squidpy/datasets/_utils.py

@@ -1,9 +1,12 @@
+from __future__ import annotations
+
 import os
 from abc import ABC, abstractmethod
+from collections.abc import Sequence
 from dataclasses import dataclass, field
 from inspect import Parameter, Signature, signature
 from pathlib import Path
-from typing import Any, Callable, Dict, Optional, Sequence, Tuple, Union
+from typing import Any, Callable, Union
 
 import anndata
 from anndata import AnnData
@@ -22,10 +25,10 @@ class Metadata(ABC):
     name: str
     url: str
 
-    doc_header: Optional[str] = field(default=None, repr=False)
-    path: Optional[PathLike] = field(default=None, repr=False)
-    shape: Optional[tuple[int, int]] = field(default=None, repr=False)
-    library_id: Optional[Union[str, Sequence[str]]] = field(default=None, repr=False)
+    doc_header: str | None = field(default=None, repr=False)
+    path: PathLike | None = field(default=None, repr=False)
+    shape: tuple[int, int] | None = field(default=None, repr=False)
+    library_id: str | Sequence[str] | None = field(default=None, repr=False)
 
     _DOC_FMT = ""
 
@@ -66,7 +69,7 @@ def _create_function(self, name: str, glob_ns: dict[str, Any]) -> None:
             glob_ns,
         )
 
-    def download(self, fpath: Optional[PathLike] = None, **kwargs: Any) -> Any:
+    def download(self, fpath: PathLike | None = None, **kwargs: Any) -> Any:
         """Download the dataset into ``fpath``."""
         fpath = str(self.path if fpath is None else fpath)
         if not fpath.endswith(self._extension):

src/squidpy/gr/__init__.py

@@ -1,5 +1,7 @@
 """The graph module."""
 
+from __future__ import annotations
+
 from squidpy.gr._build import spatial_neighbors
 from squidpy.gr._ligrec import ligrec
 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment

src/squidpy/gr/_build.py

@@ -3,9 +3,9 @@
 from __future__ import annotations
 
 import warnings
+from collections.abc import Iterable  # noqa: F401
 from functools import partial
 from itertools import chain
-from typing import Iterable, List, Tuple, Union  # noqa: F401
 
 import numpy as np
 from anndata import AnnData